I've been toying with the UNO, and decided to try a perf board with a header. When I tried to match them up across the length of the arduino with the result showing in the image below. I've highlighted the problem, showing how the pins in green don't match the holes in red in an attempt to use a header across the entire array. A standard header does match up with one pin fitting loose in the gap between the power and analog arrays.

I cannot believe digital array would be intentionally hampered, but I'm new to this, so I have to ask. Is there supposed to be a gap that disallows the use of a standard header and perf board? I got this one from NKC Electronics.